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fitness effects versus ratio of mutation counts on non-terminal and terminal branches

Interactive plot of the correlation between fitness estimates and the ratio of the counts for each amino-acid mutation on non-terminal versus terminal branches of the tree. This plot is designed to help assess whether mutations with higher fitness tend to be associated with more descendant sequences (in which case they would have a higher ratio of non-terminal to terminal counts).

Each point on the plot represents a fitness estimate for a different amino-acid mutation. The Pearson correlation coefficient and the number of mutations being correlated are shown in the upper left of the scatter plot. The mutations are stratified by whether they are nonsynonymous, synonymous, or introduce a stop codon.

You can mouse over points for details.

The minimum actual count slider below the plot indicates the total number of observed counts we require for a mutation before it is shown on the plot. The non-terminal to terminal ratio may be noisier for smaller values of this threshold, although more deleterious mutations are also expected to have lower actual counts.

The minimum expected count slider below the plot indicates how many expected counts of an an amino acid we require before making a fitness estimate. Larger values yield more accurate estimates but for fewer amino acids. So move the slider to the left to show estimates for more amino acids at lower confidence, and move it to the right to show estimates for fewer amino acids at higher confidence. Values in a range of 10 to 20 are usually sufficient to yield reasonably accurate estimates.

You can click/shift-click on specific genes in the legend below the plot to only show mutations for that gene.

The log ratio of the non-terminal to terminal counts is computed after adding a pseudocount of 0.5 to each count.

See https://github.com/jbloomlab/SARS2-mut-fitness for full computer code and data.